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The All of Us (AoU) initiative aims to sequence the genomes of over one million Americans from diverse ethnic backgrounds to improve personalized medical care. In a recent technical pilot, we compare the performance of …
Read PDFSomatic structural variations (SVs) represent a critical category of genomic mutations in hepatocellular carcinoma (HCC). However, the accurate identification of somatic SVs using short-read high-throughput sequencing is challenging. Here, we applied long-read nanopore sequencing and …
Read PDF<h4>Background</h4>The clinical diagnosis of Fabry Disease (FD) can be challenging due to the clinical heterogeneity, especially in females. Patients with FD often experience a prolonged interval between the onset of symptoms and receiving a diagnosis. …
Read PDFGenetic diagnosis of ADPKD has been challenging due to the variant heterogeneity, presence of duplicated segments, and high GC content of exon 1 in PKD1. In our reproductive center, 40 patients were still genetically undiagnosed …
Read PDFDespite the well-documented mutation spectra of β-thalassemia, the genetic variants and haplotypes of globin gene clusters modulating its clinical heterogeneity remain incompletely illustrated. Here, a targeted long-read sequencing (T-LRS) is demonstrated to capture 20 genes/loci …
Read PDFClinical genetic laboratories often require a comprehensive analysis of chromosomal rearrangements/structural variants (SVs), from large events like translocations and inversions to supernumerary ring/marker chromosomes and small deletions or duplications. Understanding the complexity of these events …
Read PDFHuman papillomaviruses (HPVs), like many other viruses, are able to integrate their genomes into the host cellular genome. This integration can activate viral oncogenes or alter the function of cellular oncogenes and tumor suppressor genes, …
Read PDFBrain tumors and genomics have a long-standing history given that glioblastoma was the first cancer studied by the cancer genome atlas. The numerous and continuous advances through the decades in sequencing technologies have aided in …
Read PDF<h4>Background</h4>Despite the widespread use of Multiplex Ligation-dependent Probe Amplification (MLPA) and Next-Generation Sequencing (NGS) in Duchenne/Becker Muscular Dystrophy (DMD/BMD), these methods have limitations when dealing with complex genetic backgrounds. Long-Read Sequencing (LRS), an emerging technology …
Read PDFAll forms of genetic variation originate from new mutations, making it crucial to understand their rates and mechanisms. Here, we use long-read sequencing from Pacific Biosciences (PacBio) to investigate de novo mutations that accumulated in …
Read PDFTandem repeat copy number variations (TR-CNVs), structural variations (SVs), and short indels have been responsible for many diseases and traits, but no tools exist to distinguish and detect these variants. In this study, we developed …
Read PDFAccurate detection of somatic structural variants (SVs) and somatic copy number aberrations (SCNAs) is critical to study the mutational processes underpinning cancer evolution. Here we describe SAVANA, an algorithm designed to detect somatic SVs and …
Read PDF<h4>Background</h4>Congenital adrenal hyperplasia (CAH) is an autosomal recessive disorder primarily caused by defects in adrenal steroidogenesis. Conventional genetic methods struggle to resolve complex structural variations and pseudogene interference in key genes like <i>CYP21A2</i>. Our study …
Read PDFLong-read sequencing (LRS) is a promising technology positioned to study the significant proportion of rare diseases (RDs) that remain undiagnosed as it addresses many of the limitations of short-read sequencing, detecting and clarifying additional disease-associated …
Read PDFStructural variants (SVs) play a critical role in shaping the diversity of the human genome, and their detection holds significant potential for advancing precision medicine. Despite notable progress in single-molecule long-read sequencing technologies, accurately identifying …
Read PDFNicotine is metabolized to cotinine by CYP2A6. CYP2A6 genotypes are associated with variations in enzymatic activity and increase the risk of developing tobacco-related diseases, including lung cancer. The high sequence similarity between CYP2A6 and CYP2A7, …
Read PDF<h4>Background</h4>Carrier screening for severe recessive genetic diseases in couples undergoing premarital examinations is a crucial strategy for reducing the incidence of birth defects and promoting reproductive health. However, many high-prevalence but genetically complex diseases cannot …
Read PDFCancer is fundamentally a disease of the genome, characterized by extensive genomic, transcriptomic, and epigenomic alterations. Most current studies predominantly use short-read sequencing, gene panels, or microarrays to explore these alterations; however, these technologies can …
Read PDFGenomic structural variants (SVs) contribute substantially to genetic diversity and human diseases<sup>1-4</sup>, yet remain under-characterized in population-scale cohorts<sup>5</sup>. Here we conducted long-read sequencing<sup>6</sup> in 1,019 humans to construct an intermediate-coverage resource covering 26 populations from …
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